RANBP2 p.Ala79=
c.237C>T · VCV4956309
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00989%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.51 | GERP -2.7, phastCons 0.083 |
| Overall | ||
| CADD | 12.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00989%
South Asian · 9/90,980 alleles
Filtering AF
0.00514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00376%
Overall
0.00155%
25/1,611,548 alleles · very rare
exomes 22/1,459,328 · genomes 3/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00989% | 10,109 |
| East Asian | 0.00893% | 11,194 |
| Remaining individualsnot grpmax-eligible | 0.00642% | 15,574 |
| European (non-Finnish) | 0.000678% | 147,455 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- RANBP2
- Protein
- p.Ala79=
- Coding
- c.237C>T
- MANE Select
- NM_006267
- Type
- single nucleotide variant
- Location
- chr2:108730870 (GRCh38)
- Gene constraint
- LOEUF 0.231 · pLI 1.00 (gnomAD)
- Residue 79
- an α-helix
Similar variants
- EDAR p.Arg358Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- RANBP2 p.Thr585Met Pathogenic/Likely pathogenic ★★ ⚠ same type
- EDAR p.Leu353Phe Uncertain significance ★★ ⚠ same type
- RANBP2 c.406-2A>G Uncertain significance ★★ same type
- RANBP2 p.Ala2337Val Uncertain significance ★★ same type
- RANBP2 p.Ala2564Ser Uncertain significance ★★ ⚠ same type
- RANBP2 p.Ala3072Val Uncertain significance ★★ ⚠ same type
- RANBP2 p.Ala534Val Uncertain significance ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ranbp2-p-ala79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown